Horticultural Plant Journal
·
2021
·
IF 3.032
Haoliang Wan,Xiaoliang Zhang,Ping Wang,Haiji Qiu,Yafei Guo,Yunjiang Cheng,Weiwei Wen
Sesquiterpene valencene is dominant in flavedo tissues of sweet oranges and imparts a unique woody aroma. However, the interaction between the biosynthetic pathways of valencene and other nutritional compounds is less studied. Sesquiterpenoids were significantly accumulated in a previously reported glossy mutant of orange (MT) than the wild type (WT), especially valencene and caryophyllene. In addition, we identified several other pathways with variations at both the transcriptional and metabolic levels in MT. It's interesting to found those up-regulated metabolites in MT, such as eukaryotic lipids, kaempferol and proline also showed strong positive correlation with valencene along with fruit maturation while those down-regulated metabolites, such as phenylpropanoid coumarins and most of the modified flavonoids exhibited negative correlation. We then categorized these shifted pathways into the ‘sesquitepenoid-identical shunt’ and the sesquitepenoid-opposite shunt’ and confirmed the classification result at transcriptional level. Our results provide important insights into the connections between various fruit quality-related properties.
研究领域:
植物学
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分子生物学
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代谢组学
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DOI
高影响因子
CHEMICAL ENGINEERING JOURNAL
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2025
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IF 13.2
Qiufeng Song,Changhong Liu,Ran Xu,Luyun Cai
Diatoms exhibit great potential for biofuels, high value-added production from wastewater and promoting carbon neutrality. Fucoxanthin is identified as the main carotenoid in diatoms, which is a photosynthetic pigment with a variety of biological activities and physiological functions. Light quality is essential for microalgal growth, photosynthesis and intracellular metabolism, and microalgal cells often respond to the effects of light to regulate their biochemical makeup. Therefore, goal of this research was to develop a strategy for altering light quality and intensity to maximize fucoxanthin generation, in line with the photoresponsive traits of Phaeodactylum tricornutum and to investigate the underlying mechanism based on metabolomics and transcriptomics. Different light qualities, culture strategies, light intensities and light ratios were explored and optimized, and the findings illustrated that the optimal fucoxanthin production was observed when under the red light during the initial phase, followed by a transition to the blue-green mixed light (60μmol m −2 s −1 ) conditions in the subsequent phase. Transcriptome and metabolome analyses showed that the light shift strategy provided sufficient energy and precursors for cell growth and fucoxanthin accumulation by enhancing the EMP pathway, TCA cycle, and light-harvesting complex in photosynthetic system. The present study provides a feasible strategy and mechanism to customize the light quality regulatory strategy to enhance biosynthesis of target bioactive compounds, and provides a theoretical basis for further investigation of the regulatory mechanism, which can provide a foundation for microalgal fucoxanthin production.
研究领域:
微藻生物学
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生物化学
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环境科学
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产品关联
DOI
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2025
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IF 11.3
Dandan Li,Xiaoyu Wang,Chen Xie,Ziwu Fan,Rui Ding,Songqi Liu,Yu Chen,Kai Yu
The widespread co−existence of triphenyl phosphate (TPhP) and heavy metals in sediments raises significant concerns. However, uncertainty still exists regarding the degradation characteristics of TPhP in the presence of cadmium (Cd). Therefore, this research was conducted to elucidate the impacts of Cd on TPhP degradation in sediments. Results showed that the biodegradation efficiency of TPhP in sediments exceeded 90 %. The identified degradation products of TPhP indicated that the degradation pathway primarily involved oxidative cleavage, hydroxylation, and methylation, which was further supported by condensed dual descriptors (CDD). However, the presence of Cd significantly inhibited TPhP degradation, with greater inhibition at higher concentrations of both TPhP and Cd. Transcriptomic analysis revealed that xenobiotic metabolism was significantly suppressed. Furthermore, pathways associated with cell motility, membrane transport, and energy metabolism were impaired. These disruptions likely contributed to the decreased degradation efficiency and prolonged half−life of TPhP. Interestingly, biomarkers in Firmicutes were enriched in the high−concentration TPhP + Cd treatment and strongly correlated with degradation−related gene expression, suggesting their significance in TPhP degradation under heavy metal stress. Overall, this research provides insights into the inhibitory effects of Cd on TPhP degradation and offers theoretical support for the bioremediation of TPhP−contaminated sediments with heavy metals.
研究领域:
环境科学
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分子生物学
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计算化学
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产品关联
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
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2022
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IF 5.911
Hui Li,Yan-yan Huang,Keren Agyekumwaa Addo,Ze-xuan Huang,Yi-gang Yu,Xing-long Xiao
The previous study indicated that cuminaldehyde (CUM) could be used as an antibacterial agent in sauced beef to reduce the propagation of Staphylococcus aureus ( S. aureus ). This research took sauced beef treated with 0.4 μL/mL CUM as the research object. Transcriptomic and proteomic methods were used to comprehensively analyze the changes in genes and proteins of S. aureus under CUM stress. A total of 258 differentially expressed genes (DEGs, 178 up-regulated and 80 down-regulated) and 384 differentially expressed proteins (DEPs, 61 up-regulated and 323 down-regulated) were found. It was observed that CUM destroyed the cell wall and cell membrane by inhibiting the synthesis of peptidoglycan and fatty acid. Low energy consumption strategies were formed by reducing glycolysis and ribosome de novo synthesis. The levels of genes and proteins associated with the glycine, serine , threonine , methionine , cysteine, and branched-chain amino acids were dramatically changed, which impaired protein synthesis and reduced bacterial viability . In addition, the up-regulated DEGs and DEFs involved in DNA replication , recombination and single-stranded DNA-binding contributed to DNA repair . Moreover, ATP-binding cassettes (ABC) transporters were also perturbed, such as the uptake of betaine and iron were inhibited. Thus, this study revealed the response mechanism of S. aureus under the stress of CUM, and provided a theoretical basis for the application of CUM in meat products.
研究领域:
微生物学
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食品科学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
CHEMISTRY & BIODIVERSITY
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2023
·Vol. 20
·期 6
·e202300204
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IF 2.9
Zhike Liang,Zhixia Chen,Xianmei Xue,Cuimin He,Xujiang Yuan
Abrus mollis (MJGC) has been used as a substitute herb for Abrus cantoniensis (JGC) in China. However, an in-depth comparison on their key metabolites and the mechanism of anti-inflammation between these two is not available. In this report, high pressure liquid chromatography equipped with mass spectrometry was applied to capture their flavonoid profiles; transcriptomics was adopted to analyze their anti-inflammatory mechanisms. The results showed that the main flavonoids in MJGC were vicenin-2, schaftoside and isoschaftoside, while those in JGC were vicenin-1 isomer and schaftoside isomer. The anti-inflammatory activity of JGC was slightly stronger than that of MJGC. The number of differential expression genes regulated by JGC was significantly higher than MJGC. JGC regulated 151 (42 up and 109 down) of inflammation related genes, while MJGC regulated 58 (8 up and 50 down) of inflammation related genes. The results of this study provided scientific evidence and guidance for the substitution of MJGC and JGC.
研究领域:
药用植物学
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药学
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转录组学
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植物化学
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DOI
PubMed
高影响因子
Aquaculture Reports
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2022
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IF 3.385
Jia Xu,Xinzhou Yao,Yingying Lin,Shuyan Chi,Shuang Zhang,Junming Cao,Beiping Tan,Shiwei Xie
Dietary low-fishmeal (FM) have negative impacts on growth performance and metabolic responses in aquatic animals, while Schizochytrium limacinum have multiple benefits due to its rich contents of docosahexaenoic acid (DHA). However, little information is available on the effects of S. limacinum on Pacific white shrimp ( Litopenaeus vannamei ) in a low-FM diet (LF). An 8-week feeding trial were used to investigate the impacts of S. limacinum on growth performance, as well as morphological changes, biochemical indicators, antioxidant capacity, and transcriptomic profiles of hepatopancreas in shrimp fed a low-FM diet. Compared to LF diet, 0.3% S. limacinum (LFLD) diet significantly decreased the specific growth rate (SGR), and did not affect the feed conversion rate (FCR) and weight gain rate (WGR); whereas 0.6% S. limacinum (LFHD) diet did not affect the SGR, FCR and WGR. Histological structures of hepatopancreas showed that LFLD and LFHD treatments reduced the number and size of secretory cells and increased the number of storage cells, compared to LF group. LFLD and LFHD diets significantly decreased the concentrations of triglyceride and total cholesterol, significantly increased the levels of glutathione peroxidase and total antioxidative capacity, while did not affect the levels of malondialdehyde and superoxide dismutase. A total of 135 differential expression genes (DEGs) were identified in LFLD group and 108 DEGs were identified in LFHD group (both compared to LF group). Administration of S. limacinum altered the transcriptomic profiles, while LFHD induced a pattern similar to that of LF. LFLD and LFHD treatments mainly affected the 9 KEGG metabolic pathways, including “Arachidonic acid metabolism” and “Glutathione metabolism”. In conclusion, LFLD treatment impaired the growth performance of shrimp, while LFHD treatment did not affect it; and both treatments improved the morphological structure, lipid accumulation and antioxidant capacity of hepatopancreas.
研究领域:
水产养殖学
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营养学
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分子生物学
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产品关联
DOI
高影响因子
Aquaculture Reports
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2022
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IF 3.385
Jia Xu,Chaozhong Zheng,Shuyan Chi,Shuang Zhang,Junming Cao,Beiping Tan,Shiwei Xie
Dietary Clostridium autoethanogenum protein (CAP) has the potential to replace fishmeal (FM), but excessive CAP substitutions will affect gut health. Bile acids (BAs) have multiple benefits, but little information is available on the effects of BAs on Pacific white shrimp ( Litopenaeus vannamei ) fed a CAP diet (CAP replacing FM). An 8-week feeding trial were used to investigate the impacts of CAP substitution and BAs addition on structural changes of intestine, apoptosis, inflammatory cytokine and NFκB pathway of intestine, and transcriptomic profiles of hepatopancreas in Pacific white shrimp. Compared to PC (control) treatment, the NC (CAP50, CAP replacing 50% FM) treatment significantly decreased the fold height (FH) and villus length (VL) of midgut, and impaired the mitochondrial cristae. Compared to NC group, the FH was increased in BA1 (CAP50 with 0.03% BAs) and BA2 (CAP50 with 0.06% BAs) groups, the muscle layer thickness (MT) was decreased in BA2 and BA3 (CAP50 with 0.09% BAs) groups, the VL was increased in BA1 group, and the mitochondrial cristae was normal and well-defined in BA1 and BA2 groups (all p < 0.05). The NC increased the genes expression of apoptosis and NFκB signalling pathway, while the BA2 decreased the genes expression of apoptosis, inflammatory cytokine and NFκB signalling pathway. In transcriptomics analysis, a total of 171 differential expression genes (DEGs) were identified in NC group and 50 DEGs in BA2 group. There was 13 DEGs was observed both in NC and BA2 groups. The 5 KEGG pathways were statistically enriched in all treatments, including “Carbon metabolism”, “One carbon pool by folate”, “Glycine, serine and threonine metabolism”, “Amino sugar and nucleotide sugar metabolism”, and “PPAR signaling pathway”. In conclusion, CAP50 substitution impaired the intestinal health and 0.06% BAs addition improved it, both treatments altered the transcriptomics profiles of hepatopancreas in Pacific white shrimp.
研究领域:
水产养殖学
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分子生物学
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营养学
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产品关联
DOI
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
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2024
·
IF 8.2
Yibo Dong,Jiaohong Li,Zhenxiang Guo,Lei Han,Jing Zhao,Xiaomao Wu,Xiangsheng Chen
Pesticides are frequently used to control target pests in the production of spice crops such as chives ( Allium ascalonicum ). However, little information is available on the responses and underlying mechanisms of pesticide exposure in this crop. Our findings revealed that the uptake, transportation, and subcellular distribution of three typical pesticides—the fungicide pyraclostrobin (PAL), insecticide acetamiprid (ATP), and herbicide pendimethalin (PND) in chives, as well as their physiological, biochemical, metabolic, and transcriptomic responses—were dependent on pesticide properties, especially hydrophobicity. The distribution of PAL and PND in chives decreased in the order root > stem > leaf, but the distribution order of ATP was the opposite. The proportion of PAL and PND in the solid phase of the root cells gradually increased, but ATP mainly existed in the cell-soluble component, indicating that the latter had an upward translocation ability and thus mainly accumulated in the leaves. Malondialdehyde levels in chive leaves were not significantly affected by exposure to these pesticides; however, the activities of superoxide dismutase (SOD) and catalase (CAT) in chive leaves increased significantly. Moreover, these pesticides exhibited critical differences in chive responses through the interaction of metabolites and regulation of differentially expressed genes. PAL dramatically influenced five carbohydrate metabolic pathways (34.35 %), disturbing the starch-to-sucrose balance. ATP strongly affected five amino acid (AC) metabolic pathways (33.38 %), enhancing four free amino acid levels. PND notably affected eight fatty acid (FA) metabolic pathways (25.38 %), increasing two unsaturated and decreasing one saturated FA. Simultaneously, PND, ATP, and PND accumulated in the chives could be detoxified through metabolic pathways mediated by cytochrome P450 (P450) and glycosyltransferase (GT)/glutathione S-transferase (GST), producing phase I (7, 4, and 5) and II (11, 13, and 10) metabolites, respectively. This study provides important molecular insights into the responses and underlying mechanisms of spice crop exposure to pesticides.
研究领域:
植物科学
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环境毒理学
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分子生物学
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
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2024
·
IF 7.7
Liangting Shao,Yang Dong,Shanshan Chen,Junsheng Sheng,Linlin Cai,Xinglian Xu,Huhu Wang
Aeromonas is a ubiquitous aquatic bacteria, and it is a significant factor contributing to meat spoilage during processing and consumption. The abilities of Aeromonas salmonicida 29 and 57, which exhibit spoilage heterogeneity, to secrete protease, lipase, hemolysin, gelatinase, amylase, and lecithinase were confirmed by plate method. A total of 3948 proteins were identified by ITRAQ in extracellular secretions of A. salmonicida , and 16 proteases were found to be potentially related to spoilage ability. The complete genome sequence of A. salmonicida 57 consists of one circular chromosome and three plasmids, while A. salmonicida 29 consists of one circular chromosome, without a plasmid. Transcriptomic analysis revealed a significant number of DEGs were up-regulated in A. salmonicida 29, which were mainly enriched in metabolic pathways (e.g., amino acid metabolism, carbohydrate metabolism), indicating that A. salmonicida 29 had better potential to decompose and utilize nutrients in meat. Six protease genes (2 pepB , hap , pepA , ftsI , and pepD ) were excavated by combined ITRAQ with transcriptome analysis, which potentially contribute to bacterial spoilage ability and exhibit universality among other dominant spoilage bacteria. This investigation provides new insights and evidence for elucidating metabolic and spoilage phenotypic differences and provides candidate genes and strategies for future prevention and control technology development.
研究领域:
微生物学
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食品科学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
Bioresources and Bioprocessing
·
2024
·Vol. 11
·期 1
·1-12
·
IF 4.3
Ke Xiang,Jiang Xing,Wang Shuohan,Tian Xiwei,Chu Ju
Comparative transcriptomics uncovered distinct expression patterns of genes associated with cofactor and vitamin metabolism in the high-yielding mutant strain Saccharopolyspora erythraea HL3168 E3, as compared to the wild-type NRRL 2338. An in-depth analysis was conducted on the effects of nine vitamins, and it was determined that thiamine pyrophosphate (TPP), vitamin B2, vitamin B6, vitamin B9, vitamin B12, and hemin are key enhancers in erythromycin production in E3, increasing the erythromycin titer by 7.96–12.66%. Then, the Plackett-Burman design and the path of steepest ascent were applied to further optimize the vitamin combination for maximum production efficiency, enhancing the erythromycin titer in shake flasks by 39.2%. Otherwise, targeted metabolomics and metabolic flux analysis illuminated how vitamin supplementation modulates the central carbon metabolism with notable effects on the TCA cycle and methionine synthesis to augment the provision of energy and precursors essential for erythromycin synthesis. This work highlights the capacity for precise vitamin supplementation to refine metabolic pathways, thereby boosting erythromycin production, and provides valuable directions for application on an industrial scale. Graphical
研究领域:
微生物学
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生物技术
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代谢工程
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产品关联
DOI
PubMed
高影响因子
BMC PLANT BIOLOGY
·
2025
·Vol. 25
·期 1
·1-27
·
IF 4.8
Wang Pei-lu,You Jin-ling,Hua Qian-ming,Li Hua-qiang,Shi Qi,Li Wen-long,Sheng Yun-jie,Liu Kao-hua,He Bing-qian,Zhang Qiao-yan,Qin Lu-ping,Meng Xiong-yu
Background Eucommia ulmoides Oliver is a dioecious plant with great economic value, but the underlying metabolite mechanism difference between male and female E. ulmoides remain poorly understood.Results In this study, we integrated a dual-platform metabolomics approach with transcriptomics to systematically analyze differences in metabolite and gene expression in the cortex and leaves of male and female E. ulmoides. As a result, 1,452 metabolites (603 volatile, 849 non-volatile) were characterized, and 156 and 129 differentially accumulated metabolites were identified in FEC vs. MEC and FEF vs. MEF, respectively. The expression of key genes (PLA2G4, DOXs, LOX2S, and CEQORH) involved in alpha-linolenic acid metabolism was significantly altered in MEC. Similarly, the expression of key genes (CHS, FLS, DFR, and ANR) involved in flavonoid biosynthesis was significantly altered in MEF.Conclusion sOur findings shed light on the metabolite mechanism behind the metabolic differences between male and female E. ulmoides and contribute to the exploration of value utilization.
研究领域:
植物学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
Systems Microbiology and Biomanufacturing
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2022
·
IF 0
Shen Yi,Ke Xia,Pan Zi-Hao,Cao Li-Sha,Liu Zhi-Qiang,Zheng Yu-Guo
With staggering progress on genetic manipulation strategies, Saccharomyces cerevisiae is becoming an ideal cell factory for the de novo biosynthesis of lipid compounds. However, due to their hydrophobicity, lipids tend to be accumulated within intracellular spaces and cause a high burden on cell activity and induce product inhibition effect, which ultimately restricted the lipids biomanufacturing for industrial application. Herein, an oleic acid stress (OAS) model was applied for the long-time domestication of BY4741 cells, and a subclone of A-22 was obtained through a series of acclimation (0.1% glucose and 0.2% oleic acid), showing increased accumulation of both biomass and intracellular lipid droplets compared to WT. Comparative transcriptome analysis indicated that compared to fatty acid metabolism, most transcripts enriched in the pathways of glucose catabolism (glycolysis and citrate cycle) and lipid synthesis (phospholipid and sterol) were down-regulated under OAS. While interestingly, most the above transcripts tended to be ‘restored’ in adapted strain A-22. In addition, for physical adaptation, significant increase of phosphatidylcholines was identified by lipidomic analysis, which probably caused the subsequent subcellular expansion of peroxisomes and lipid droplets as observed in the adapted strain, since phosphatidylcholines are the major constituent of their membranes. The present study systematically investigated both the phenotype change and molecular mechanism on adaptation of S. cerevisiae towards oily environment. Detailed information on functional transcripts may provide novel rational modification targets to reinforce the hydrophobic lipids biosynthesis within S. cerevisiae engineered cell factory.
研究领域:
微生物学
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生物化学与分子生物学
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系统生物学
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DOI
危险品化学品经营许可证（带存储）